scholarly journals New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1373
Author(s):  
Sewalem Tsehay ◽  
Rodomiro Ortiz ◽  
Eva Johansson ◽  
Endashaw Bekele ◽  
Kassahun Tesfaye ◽  
...  
Keyword(s):  
Population Genetics ◽  
Snp Markers ◽  
Oilseed Crop ◽  
Nucleotide Polymorphisms ◽  
Guizotia Abyssinica ◽  
Genomic Resources ◽  
Genetics Research ◽  
Specific Pcr ◽  
Kasp Assay ◽  
Hardy Weinberg Equilibrium

The development and use of genomic resources are essential for understanding the population genetics of crops for their efficient conservation and enhancement. Noug (Guizotia abyssinica) is an economically important oilseed crop in Ethiopia and India. The present study sought to develop new DNA markers for this crop. Transcriptome sequencing was conducted on two genotypes and 628 transcript sequences containing 959 single nucleotide polymorphisms (SNPs) were developed. A competitive allele-specific PCR (KASP) assay was developed for the SNPs and used for genotyping of 24 accessions. A total of 554 loci were successfully genotyped across the accessions, and 202 polymorphic loci were used for population genetics analyses. Polymorphism information content (PIC) of the loci varied from 0.01 to 0.37 with a mean of 0.24, and about 49% of the loci showed significant deviation from the Hardy-Weinberg equilibrium. The mean expected heterozygosity was 0.27 suggesting moderately high genetic variation within accessions. Low but significant differentiation existed among accessions (FST = 0.045, p < 0.0001). Landrace populations from isolated areas may have useful mutations and should be conserved and used in breeding this crop. The genomic resources developed in this study were shown to be useful for population genetics research and can also be used in, e.g., association genetics.

scholarly journals Identification of SNP markers associated with antler growth rate in sika deer (Cervus nippon)

2020 ◽  
Author(s):  
Pengfei Hu ◽  
Yongyan Deng ◽  
Hengxing Ba ◽  
chunyi li
Keyword(s):  
Growth Rate ◽  
Sika Deer ◽  
Cervus Nippon ◽  
Snp Markers ◽  
Whole Genome Sequencing Data ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Animal Genetic Resources ◽  
Antler Growth ◽  
Hardy Weinberg Equilibrium

Abstract Sika deer (Cervus nippon) constitutes one of the most valuable animal genetic resources in east Asia. The aim of this study was to identify and validate single nucleotide polymorphisms (SNPs) from antler growth-related genes of sika deer. The whole genome sequencing data of sika deer were used to identify SNP markers. Among them, 31 SNPs from antler growth-related genes exhibited significant polymorphism using genotyping by mass spectrometry. The observed and expected heterozygosities were ranged from 0.147 to 0.997 and 0.201 to 0.500, respectively. Significant deviation from the Hardy-Weinberg equilibrium was observed in 6 loci. These findings provide effective molecular detection markers for the study of variation in antler growth rate of sika deer.

scholarly journals Development a Set of 46 SNP Markers for the Yellow Catfish (Tachysurus Fulvidraco)

2021 ◽  
Author(s):  
Huaxing Zhou ◽  
Tingshuang Pan ◽  
Huan Wang ◽  
He Jiang ◽  
Jun Ling ◽  
...  
Keyword(s):  
Snp Markers ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Yellow Catfish ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Expected Heterozygosity ◽  
Hardy Weinberg Equilibrium ◽  
Whole Genome Resequencing ◽  
Tachysurus Fulvidraco

Abstract The whole genome resequencing was used to develop single nucleotide polymorphisms (SNP) markers for the yellow catfish (Tachysurus fulvidraco). A total of 46 SNP markers were selected from 5550676 genotyping markers which distributed on 26 chromosomes. Of the 46 SNPs analyzed, 35 SNPs conformed to Hardy-Weinberg equilibrium. The observed and expected heterozygosity of these markers ranged from 0.2519 to 0.771 and from 0.265 to 0.5018, respectively. This set of markers will be of great useful for population genetics of the yellow catfish.

scholarly journals Presence of the HPPD Inhibitor Sensitive 1 Gene and ALSS653N Mutation in Weedy Oryza sativa Sensitive to Benzobicyclon

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1576
Author(s):  
Chad Brabham ◽  
Jason K. Norsworthy ◽  
Fidel González-Torralva
Keyword(s):  
Weedy Rice ◽  
Japonica Rice ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Herbicide Resistant ◽  
Rice Plants ◽  
Specific Pcr ◽  
Kasp Assay ◽  
Allele Specific ◽  
Allele Specific Pcr

Benzobicyclon has shown varying results in controlling weedy rice, including those with imidazolinone (IMI) resistance. Tolerance to benzobicyclon in cultivated japonica rice, but not indica or aus-like cultivars, is conferred by a fully functional HPPD Inhibitor Sensitive 1 (HIS1) gene. Herein, a diagnostic Kompetitive Allele Specific PCR (KASP) assay was developed to predict the HIS1 genotype of weedy rice plants from 37 accessions and correlated to their response to benzobicyclon in the field. Two-thirds of the 693 weedy rice plants screened were tolerant to benzobicyclon (371 g ai ha−1, SC formulation) at 30 days after treatment (DAT). Thirty-four percent of plants were homozygous for the HIS1 allele and 98% of these plants exhibited field tolerance. However, the his1 genotype did not always correlate with field data. Only 52% of his1 plants were considered sensitive, indicating that the single nucleotide polymorphisms (SNPs) chosen in the KASP assay are not a reliable tool in predicting his1 homozygous plants. In an additional experiment, 86% of the 344 plants with at least one copy of the ALSS653N trait harbored a HIS1 allele, suggesting fields infested with IMI herbicide-resistant weedy rice are unlikely to be controlled with benzobicyclon.

scholarly journals Development of Breeder-Friendly KASP Markers for Low Concentration of Kunitz Trypsin Inhibitor in Soybean Seeds

2021 ◽  
Vol 22 (5) ◽  
pp. 2675
Author(s):  
M. Luciana Rosso ◽  
Chao Shang ◽  
Qijian Song ◽  
Diana Escamilla ◽  
Jay Gillenwater ◽  
...  
Keyword(s):  
Trypsin Inhibitor ◽  
Protein Digestibility ◽  
Population Based ◽  
Hplc Method ◽  
Snp Markers ◽  
Soybean Seeds ◽  
Kunitz Trypsin Inhibitor ◽  
Breeding Lines ◽  
Specific Pcr ◽  
Kasp Assay

Trypsin inhibitors (TI), a common anti-nutritional factor in soybean, prevent animals’ protein digestibility reducing animal growth performance. No commercial soybean cultivars with low or null concentration of TI are available. The availability of a high throughput genotyping assay will be beneficial to incorporate the low TI trait into elite breeding lines. The aim of this study is to develop and validate a breeder friendly Kompetitive Allele Specific PCR (KASP) assay linked to low Kunitz trypsin inhibitor (KTI) in soybean seeds. A total of 200 F3:5 lines derived from PI 547656 (low KTI) X Glenn (normal KTI) were genotyped using the BARCSoySNP6K_v2 Beadchip. F3:4 and F3:5 lines were grown in Blacksburg and Orange, Virginia in three years, respectively, and were measured for KTI content using a quantitative HPLC method. We identified three SNP markers tightly linked to the major QTL associated to low KTI in the mapping population. Based on these SNPs, we developed and validated the KASP assays in a set of 93 diverse germplasm accessions. The marker Gm08_44814503 has 86% selection efficiency for the accessions with low KTI and could be used in marker assisted breeding to facilitate the incorporation of low KTI content in soybean seeds.

scholarly journals Identification and Development of KASP Markers for Novel Mutant BnFAD2 Alleles Associated With Elevated Oleic Acid in Brassica napus

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Fu ◽  
Annaliese S. Mason ◽  
Yaofeng Zhang ◽  
Huasheng Yu
Keyword(s):  
Oleic Acid ◽  
Acid Content ◽  
Allelic Variation ◽  
Fatty Acid Desaturase ◽  
Snp Markers ◽  
Oleic Acid Content ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Kasp Markers

The fatty acid desaturase FAD2 genes are the main contributors to oleic acid content, and different FAD2 alleles can result in different oleic acid contents in rapeseed oil. Hence, identification of allelic variation in FAD2 is an extremely desirable breeding goal. By performing QTL mapping using 190 F2:3 lines genotyped by genome-wide single nucleotide polymorphism (SNP) markers assayed by the Brassica 60 K Infinium BeadChip Array, four quantitative trait loci (QTL) for C18:1 content were mapped on chromosomes A01, A05, A09 and C05 over 3 years in a population segregating for oleic acid content. Two BnFAD2 genes on A05 and C05 were anchored within the QTL intervals, explaining 45–52 and 15–44% of the observed variation for C18:1 content. Sequence polymorphisms between the corresponding coding regions of the parental lines found two single-nucleotide polymorphisms (SNPs) in BnFAD2.A05 and BnFAD2.C05, respectively, which led to the amino acid changes (C421T and G1073E) in the corresponding proteins. The mutation sites of Bnfad2.A05 and Bnfad2.C05 alleles were located within the second H-box and near the third H-box motif of the protein, respectively, and were found to be novel mutant alleles. Lines resulting from the combination of these two alleles contained up to 88% oleic acid in their seed oil, compared with 63% in wild-type controls. Two competitive allele-specific PCR (KASP) markers based on these two mutation sites were successfully developed and validated in segregating F2 populations. These markers will facilitate breeding for ultra-high seed oleic acid content in oilseed rape.

Identification and Development of KASP Markers for Novel Mutant BnFAD2 Alleles Associated with Elevated Oleic Acid in Brassica napus

2021 ◽  
Author(s):  
Ying Fu ◽  
Annaliese S. Mason ◽  
Yaofeng Zhang ◽  
Huasheng Yu
Keyword(s):  
Oleic Acid ◽  
Acid Content ◽  
Allelic Variation ◽  
Fatty Acid Desaturase ◽  
Snp Markers ◽  
Oleic Acid Content ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Kasp Markers

Abstract The fatty acid desaturase FAD2 genes are the main contributors to oleic acid content, and different FAD2 alleles can result in different oleic acid contents in rapeseed oil. Hence, identification of allelic variation in FAD2 is an extremely desirable breeding goal. By performing QTL mapping using 190 F2:3 lines genotyped by genome-wide single nucleotide polymorphism (SNP) markers assayed by the Brassica 60 K Infinium BeadChip Array, four quantitative trait loci (QTL) for C18:1 content were mapped on chromosomes A01, A05, A09 and C05 over three years in a population segregating for oleic acid content. Two BnFAD2 genes on A05 and C05 were anchored within the QTL intervals, explaining 45–52% and 15–44% of the observed variation for C18:1 content. Sequence polymorphisms between the corresponding coding regions of the parental lines found two single-nucleotide polymorphisms (SNPs) in BnFAD2.A05 and BnFAD2.C05, respectively, which led to the amino acid changes (C421T and G1073E) in the corresponding proteins. The mutation sites of Bnfad2.A05 and Bnfad2.C05 alleles were located within the second H-box and near the third H-box motif of the protein, respectively, and were found to be novel mutant alleles. Lines resulting from the combination of these two alleles contained up to 88% oleic acid in their seed oil, compared with 63% in wild-type controls. Two competitive allele-specific PCR (KASP) markers based on these two mutation sites were successfully developed and validated in segregating F2 populations. These markers will facilitate breeding for ultra-high seed oleic acid content in oilseed rape.

Monitoring of Hematopoietic Chimerism by Real-Time Quantitative PCR of Single Nucleotide Polymorphisms In Samples with Low DNA Quantities.

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3491-3491
Author(s):  
Christian Bach ◽  
Elmira Tomova ◽  
Katja Goldmann ◽  
Birgit Lauer ◽  
Wolf Roesler ◽  
...  
Keyword(s):  
Real Time ◽  
Conflicts Of Interest ◽  
Quantitative Polymerase Chain Reaction ◽  
Snp Markers ◽  
Limiting Factor ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Hematopoietic Stem ◽  
Real Time Quantitative Pcr ◽  
Specific Pcr

Abstract Abstract 3491 Novel methods to quantify chimerism after allogeneic hematopoietic stem cell transplantation (HSCT) based on single-nucleotide polymorphism (SNP) specific real-time quantitative polymerase chain reaction (qPCR) require high amounts of input DNA. The applicability of these methods in cases where DNA quantity is limiting, however, is currently unclear. Here, we demonstrate that SNP typing performed with just 5ng of input DNA still allowed for the distinction of positive (mean ct 28.05) and negative (ct > 36) signals. In addition, we confirm the high informative value of a set of 19 SNP markers, with 12 markers exceeding 20% informativity in our population (n=74). Of interest, a four-fold reduction of input DNA for qPCR standard curves did not alter PCR efficiencies. Most importantly, in 7 out of 16 allogeneic HSCT patients who experienced disease relapse, a retrospective analysis using the SNP-qPCR method revealed re-appearance of recipient chimerism earlier (mean 95 days) compared to previous results obtained by a short tandem repeat (STR) specific PCR. Taken together our data clearly demonstrate that SNP-qPCR is more sensitive compared to the widely used STR-PCR even with reduced amounts of input DNA. We therefore recommend that SNP-qPCR is preferable to STR-PCR for chimerism analysis in cases where DNA quantity is a limiting factor. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Development and characterization of 57 SNP markers in Misgurnus anguillicaudatus

2021 ◽  
Author(s):  
Guiyun Huang ◽  
Fengying Gao ◽  
Zhigang Liu ◽  
Jianmeng Cao ◽  
Gang Chen ◽  
...  
Keyword(s):  
Snp Markers ◽  
Freshwater Species ◽  
Nucleotide Polymorphisms ◽  
Misgurnus Anguillicaudatus ◽  
Population Genetic Analysis ◽  
Single Nucleotide ◽  
Natural Resource Conservation ◽  
Hardy Weinberg Equilibrium ◽  
Selection Of

Abstract The dojo loach Misgurnus anguillicaudatus is an endemic freshwater species to Asia. The effective conservation and molecular-aided selection of M. anguillicaudatus have been limited without sufficient molecular markers. In this study, 112 novel single nucleotide polymorphisms (SNPs) were screened based on 2b-RAD sequencing database, and 57 SNP markers were developed and characterized by genotyping 40 individuals using SNaPshot method. The observed heterozygosity (Ho) ranged from 0.025 to 0.675, while the expected heterozygosity (He) varied from 0.025 to 0.500. The minor allele frequency (MAF) ranged from 0.013 to 0.500. Among these SNPs, 18 loci were found to deviate significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05). The first set of SNP markers developed from M. anguillicaudatus will provide valuable information in further population genetic analysis and natural resource conservation.

Genetic structure of Patagonian toothfish populations from otolith DNA

2016 ◽  
Vol 28 (5) ◽  
pp. 347-360 ◽  
Author(s):  
Lola Toomey ◽  
Dirk Welsford ◽  
Sharon A. Appleyard ◽  
Andrea Polanowski ◽  
Cassandra Faux ◽  
...  
Keyword(s):  
Population Genetics ◽  
Genetic Differentiation ◽  
High Throughput Sequencing ◽  
Nucleotide Polymorphisms ◽  
Nuclear Markers ◽  
Genetic Stock ◽  
Mitochondrial Markers ◽  
Genetics Research ◽  
Spatial Coverage ◽  
Patagonian Toothfish

AbstractThe Patagonian toothfish, Dissostichus eleginoides, is a valuable fishery species and has a discontinuous distribution across the Southern Ocean. Identification of the genetic stock structure of toothfish would allow evaluation of the suitability of the spatial scale at which fisheries management operates. Genetic subdivision seems likely given the species distribution. Population genetics studies of this species have been performed; however, they have been limited by sample size, spatial coverage and/or the type of markers investigated. As a potential solution, we developed methods for extracting toothfish DNA from otoliths that are available in large numbers from collections held at several research institutes. Genetic differentiation between the three oceanic sectors was investigated. Four mitochondrial and four nuclear markers with multiple single nucleotide polymorphisms were sequenced by high throughput sequencing for samples from six locations. Genetic differentiation was found between three sectors with nuclear markers. However, only the Pacific sector was differentiated from other sectors with mitochondrial markers. This study demonstrates the usefulness of otolith DNA as a means of increasing sample sizes for population genetics research of fish. Additionally, the combination of nuclear and mitochondrial markers may allow insight into how the observed differences in movements between male and female toothfish impact population structure.

scholarly journals Single Nucleotide Polymorphism Analysis Using KASP Assay Reveals Genetic Variability in Rotylenchulus reniformis

Plant Disease ◽  
2019 ◽  
Vol 103 (8) ◽  
pp. 1835-1842 ◽  
Author(s):  
Churamani Khanal ◽  
Manjula T. Kularathna ◽  
Jeffery D. Ray ◽  
Salliana R. Stetina ◽  
Edward C. McGawley ◽  
...  
Keyword(s):  
South Carolina ◽  
Genetic Variability ◽  
Resistance Breeding ◽  
Snp Markers ◽  
Polymorphism Analysis ◽  
Nucleotide Polymorphisms ◽  
Reniform Nematode ◽  
Rotylenchulus Reniformis ◽  
Single Nucleotide ◽  
Specific Pcr

This study employed single nucleotide polymorphisms (SNPs) to determine the genetic variability present in 26 isolates of Rotylenchulus reniformis from Louisiana, Mississippi, Arkansas, South Carolina, Georgia, Hawaii, and Alabama. Genomic DNA from reniform nematode was extracted and increased quantitatively using the process of whole genome amplification. More than 162 putative SNPs were identified, 31 of which were tested using a KASP kompetitive allele-specific PCR genotyping assay. Of the SNPs tested, 13, 17, and 19 SNPs revealed genetic variability within reniform nematode isolates from Louisiana, Mississippi, and Arkansas, respectively. Seven SNPs elucidated genetic differences among isolates of reniform nematode from Louisiana, Mississippi, and Arkansas. Eight SNPs determined genetic variability among individual isolates from South Carolina, Georgia, Hawaii, and Alabama. This study is the first to report genetic variability in geographic isolates of reniform nematode employing a SNP assay. This study also demonstrated that SNP markers can be used to evaluate isolates of R. reniformis and could be useful to assess their genetic diversity, origin, and distribution. Such information would be extremely useful in resistance breeding programs.

Sign in / Sign up

Export Citation Format

Share Document